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Thursday, November 1, 2018

Publication Roundup: CLC Genomics Workbench

Publication Roundup: CLC Genomics 

Check out these recent articles citing CLC Genomics Workbench, a comprehensive, easy-to-use toolbox that ensures continuity in your NGS analysis workflow.  Below are a few examples of how researchers from India to Australia are using CLC Genomics Workbench as a tool to decipher disease, improve vaccines, and identify potentially harmful pathogens.


Equine Encephalosis Virus in India, 2008
First author: Pragya D. Yadav

To determine whether Equine Encephalosis Virus (EEV) had surfaced in India in 2008, a team there used updated tools, including CLC Genomics Workbench, to analyze raw data from necropsy blood and lung samples of a potentially infected horse. They conducted reference sequence mapping for the RNA reads of the infectious agent, using CLC Genomics Workbench to develop a reference-guided assembly program. Identifying and generating the complete EEV genome enabled the team to confirm its presence—and to reiterate control measures against the virus. Read about the study, which ran in the CDC’s Emerging Infectious Diseases journal, here.


Bioreactor Virome Metagenomics Sequencing using DNA Spike-Ins
First author: Geert Cremers

Though microbial research is historically culture-based, researchers today are using NGS techniques to determine the presence of microbial communities without the need for cultivation. Bioinformatical research on viruses remains limited because of the small amounts of viral DNA that can be obtained by analysis. The February issue of PeerJ ran a report by a Dutch team who used CLC Genomics Workbench for bioinformatics information while sequencing the virome of a bioreactor. They compared results of both DNA-spiking of samples with MDA-amplified samples, and ultimately determined that DNA-spiking might be a low-bias, simple, inexpensive alternative for sequencing metagenomes which include low amounts of DNA.


Transcriptomic Analysis of Ehrlichia Ruminantium During the Developmental Stages in Bovine and Tick Cell Culture
First author: Mabotse A.Tjale

A South African team researched possible improvements to the currently available vaccine for heartwater—a non-contagious, tick-borne disease which poses a significant threat to ruminant livestock. The team performed a genome-wide transcriptional profile of Ehrlichia ruminantium, using CLC Genomics Workbench to process and analyze RNA-seq data. Their findings, published in the January 2018 issue of Ticks and Tick-Borne Diseases, concluded that several E. ruminantium genes were differentially expressed, and identified pathways that seemed significant to its development and pathogenicity.


Clonal Diversity and Geographic Distribution of Methicillin-Resistant Staphylococcus Pseudintermedius from Australian Animals: Discovery of Novel Sequence Types

First author: Kate A. Worthing

A group of veterinary life science researchers used whole genome sequencing to confirm that both internationally-established and novel clones of methicillin-resistant Staphylococcus pseudintermedius (MSRP) were present in Australia. MSRP is an increasingly prevalent pathogen in the veterinary field, and the team was hoping to understand treatment options and the propensity for horizontal transfer of genetic resistance, which could endanger public health. In their findings, published in Veterinary Microbiology, they outlined the molecular epidemiology of 77 MSRP isolates collected from Australian companion animals, and mentioned using CLC Genomics Workbench for de novo assembly, molecular typing and resistance gene detection. Their conclusion argues that due to the bond between people and their pets, there is a pressing need for veterinary medicine to use antimicrobials to avoid severe human infection due to MSRP.


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